Re: [Freesurfer] aparc.pial.stats

[Ting Li]

External Email - Use Caution

Thank you so much! It is really helpful.

Best regards,
Ting Li
> On May 9, 2019, at 3:15 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> You can use aparcstats2table, just specify   -p aparc.pial
> 
> On 5/8/19 11:17 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer Expert,
>> 
>> Is there a way to get the aparc.pial.stats in one command like 
>> aparcstats2table?
>> 
>> Thanks a lot!
>> 
>> Best regards,
>> Ting
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] units for tracula output

[Alexopoulos, Dimitrios]

External Email - Use Caution

What units are the diffusion measures generated by tracula that are found in  
the files named
"pathstats.overall.txt". For example, as 10^-3

Jim


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Primary slice direction and image origin?

[Greve, Douglas N.,Ph.D.]

It looks at the RAS of the direction cosines for the direction going 
from one slice to the next. If the absolute value of the R component is 
the max of the three, then it is assigned to be sagittal. If the A 
component is max, then it's coronal. If S, then axial

On 5/9/19 5:52 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Thanks Doug, I think I may have resolved my orientation / transformation 
> issue.
>
> Do you happen to know how the primary slice direction is determined?
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Greve, Douglas 
> N.,Ph.D.
> Gesendet: Freitag, 3. Mai 2019 17:31
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>
> You can get the image position from tag 20 32. It might not match what you 
> see in mri_info because we use RAS and dicom uses something else (LPS maybe), 
> so the "first voxel" might not be the same.
>
>
> On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote:
>>   External Email - Use Caution
>>
>> Hi Doug,
>>
>> thanks for your answer. I know how to print the slice direction, however, as 
>> there is no DICOM tag directly related to it, it has to be determined from 
>> some information of the DICOM header. I was wondering which these are.
>>
>> Same for the image origin or the voxel to ras transform in general:
>> voxel to ras transform:
>>   0.9367   0.0327   0.0240  -111.2289
>>  -0.0206   0.8545  -0.4108   -82.6730
>>  -0.0339   0.3843   0.9114  -121.5813
>>   0.   0.   0. 1.
>>
>> In that transform the last column indicates the image's origin. However, I 
>> was unable to find the relation between the information available in the 
>> DICOM header and this transform.
>>
>> Best,
>> Falk
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  Im Auftrag von Greve, Douglas 
>> N.,Ph.D.
>> Gesendet: Donnerstag, 2. Mai 2019 17:33
>> An: freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>>
>> You can use --slicedirection to get the slice direction (it will also get 
>> printed out by just running mri_info on a file). What do you mean by the 
>> image origin?
>>
>> On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>>>   External Email - Use Caution
>>>
>>> Dear all,
>>>
>>> This is not directly related to FreeSurfer, however, can anyone tell
>>> me how the primary slice direction and image origin is determined
>>> from the DICOM header as displayed for example using mri_info?
>>>
>>> Best,
>>>
>>> Falk
>>>
>>> ...
>>>
>>> klinikum_logo_schmal_e-mail_blau
>>>
>>> *Universitätsklinik für Neurologie*
>>>
>>>
>>> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät
>>> Leipziger Str. 44
>>> 39120 Magdeburg
>>>
>>> *Telefon: *+49-391-6117-512
>>>
>>> *falk.luesebr...@med.ovgu.de *
>>> *http://www.kneu.ovgu.de/kneu.html*
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] aparc.pial.stats

[Greve, Douglas N.,Ph.D.]

You can use aparcstats2table, just specify   -p aparc.pial

On 5/8/19 11:17 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Expert,
>
> Is there a way to get the aparc.pial.stats in one command like 
> aparcstats2table?
>
> Thanks a lot!
>
> Best regards,
> Ting
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: Visualizing Volumetric Files on Surface

[Ruopeng Wang]

Hi Maedeh,

I'm not quite clear about what exactly you want to do but have you tried 
loading the volume as an overlay to the surface in freeview?

Best,
Ruopeng

On 5/9/19 12:47 PM, Maedeh Khalilian wrote:
>  External Email - Use Caution
>
>> From: "Maedeh Khalilian" 
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Date: Thu, 09 May 2019 01:24:58 +0430
>> Subject: Visualizing Volumetric Files on Surface
>> Dear FreeSurfer experts;
>> I have created some volumetric(.nii) files in FreeSurfer (the procedure
>> is
>> as following: lh/rh.aparc.annot> mri_divide_parcellation >
>> mri_aparc2aseg >
>> deleting subcortical and white matter regions in order to keep just
>> cortical
>> regions on GM).
>>
>> Now I wanna visualize my volumetric files on surface so that I myself
>> can
>> determine the color of each region. But I dunno how to do it exactly.
>>   I would be grateful if u could help me with that.
>> Thanks in advance
>> Best regards
>> Maedeh,
>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Fwd: Visualizing Volumetric Files on Surface

[Maedeh Khalilian]

External Email - Use Caution

> From: "Maedeh Khalilian" 
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Date: Thu, 09 May 2019 01:24:58 +0430
> Subject: Visualizing Volumetric Files on Surface 

> Dear FreeSurfer experts;
> I have created some volumetric(.nii) files in FreeSurfer (the procedure
> is 
> as following: lh/rh.aparc.annot> mri_divide_parcellation >
> mri_aparc2aseg > 
> deleting subcortical and white matter regions in order to keep just
> cortical 
> regions on GM).
> 
> Now I wanna visualize my volumetric files on surface so that I myself
> can 
> determine the color of each region. But I dunno how to do it exactly.  
>  I would be grateful if u could help me with that.
> Thanks in advance
> Best regards
> Maedeh,
> 
> 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] PostDoc position in Population Neuroimaging available, Connectivity Group, Research Centre Jülich (Germany)

[Svenja Caspers]

   External Email - Use Caution

The Connectivity Group (lead: Prof. Dr. Svenja Caspers) of the Institute 
of Neuroscience and Medicine (INM-1), Research Centre Jülich (Germany) 
is seeking applications for a


*PostDoctoral Research Position in Population Neuroimaging*

**

(E 13 TVöD; 39 hours/week)

The Connectivity Group focuses on the investigation of brain variability 
throughout the life span in relation to environmental and genetic 
factors, with a particular focus on the aging brain and taking advantage 
of large population-based cohorts who underwent MR neuroimaging (e.g. UK 
Biobank, German National Cohort, Human Connectome Project, 1000BRAINS). 
Specific aspects include structural, resting-state functional 
connectivity as well as advanced diffusion imaging for structural 
connectivity analyses, including graph-theory analyses. Large cohorts of 
thousands of subjects are processed using adjusted pipelines and 
workflows for high-throughput imaging analytics based on common software 
packages (e.g. FreeSurfer, FSL, MRtrix) on available high-performance 
computing systems of the Research Centre Jülich. Current interests cover 
topics in advanced statistical analyses and data-driven methods using 
machine-learning and deep learning approaches. These efforts are part of 
current projects within the Human Brain Project (HBP).


The successful candidate has a PhD in neuroscience, computer science, 
psychology, medicine or related fields and has experience with 
processing and analyses of MR neuroimaging data in larger cohorts. A 
strong interest and expertise in applying machine-learning to large 
neuroimaging datasets is highly desired to enable the candidate to 
conduct novel and innovative research projects to understand the normal 
variability of brain aging.


Your profile:

- deep knowledge of several software packages for processing of 
neuroimage data (e.g. FreeSurfer, FSL, MRtrix), also including 
respective python packages (e.g. NiPy, DiPy) and longitudinal pipelines


- profound expertise in multivariate statistical analyses, including 
usage of software for large-scale statistical analyses (e.g. R) and 
modelling of non-linear and longitudinal effects


- profound programming skills (e.g. Python) enabling high-throughput big 
data analyses


- knowledge of and interest in machine-learning and deep-learning 
techniques to be applied to large neuroimage datasets of 
population-based cohorts


- familiarity in working with large datasets

- strong publication track record

- ability to work independently

- high proficiency in English

The applicant will become part of an interdisciplinary team of PostDocs, 
PhD and MD students with various backgrounds. He / she will have ample 
possibilities to expand his / her own knowledge and expertise and 
interact and collaborate with colleagues from different fields, 
including big data analytics, genetics, epidemiology and microscopic 
analyses. With our group closely collaborating with the Jülich 
Supercomputing Center, the applicant will join current efforts in 
bringing population neuroimaging analytics to high-performance computing 
clusters for efficient and novel analyses approaches. The applicant will 
be involved in the supervision and mentoring of PhD, MD, master and 
bachelor students.


Funding for the position is available for two years. Applications will 
continue to be received until the position is filled.


Please send your comprehensive application, including CV, publication 
record, copies of relevant certificates and either reference letters or 
names of two potential references to Prof. Dr. Svenja Caspers 
(s.casp...@fz-juelich.de ).



--
==
*Univ.-Prof. Dr. med. Dr. rer. pol. Svenja Caspers *

   Direktorin Institut für Anatomie I
   Heinrich-Heine-Universität Düsseldorf
   40221 Düsseldorf (Deutschland)
   Tel.: 0211-8112678
   Email: svenja.casp...@hhu.de
svenja.casp...@med.uni-duesseldorf.de

/und /

   Arbeitsgruppe Konnektivität
   Institut für Neurowissenschaften und Medizin (INM-1)
   Forschungszentrum Jülich GmbH
   52425 Jülich (Deutschland)
   Tel.: 02461-611742
   Email: s.casp...@fz-juelich.de



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Questions about registration

[Yang, Weiqi]

Hi,


I am new to Free Surfer and am working on the resting state fMRI data analysis 
using FS-FAST. When I used the tkregister-sess command to see the registration 
quality (from structural image to fMRI image), I found that there is one 
registration not good (QA value = 0.9). So I did manual registration and save 
the reg. However, I don't know how to use my manual registration file as input 
for the bbregistration. My solution is that I overwrote the original 
registration file and ran the automatic registration again. Is there any neater 
way to do this? How to check the QA value for the updated registration?


And I also found there are registration files in both fsd directory (ex. BOLD ) 
and the session directory (ex. 001). Are these registration files the same?


Thank you in advance for your time.


Best,

Weiqi
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Primary slice direction and image origin?

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Thanks Doug, I think I may have resolved my orientation / transformation issue.

Do you happen to know how the primary slice direction is determined?

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Greve, Douglas N.,Ph.D.
Gesendet: Freitag, 3. Mai 2019 17:31
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Primary slice direction and image origin?

You can get the image position from tag 20 32. It might not match what you see 
in mri_info because we use RAS and dicom uses something else (LPS maybe), so 
the "first voxel" might not be the same.


On 5/3/2019 3:01 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Hi Doug,
>
> thanks for your answer. I know how to print the slice direction, however, as 
> there is no DICOM tag directly related to it, it has to be determined from 
> some information of the DICOM header. I was wondering which these are.
>
> Same for the image origin or the voxel to ras transform in general:
> voxel to ras transform:
>  0.9367   0.0327   0.0240  -111.2289
> -0.0206   0.8545  -0.4108   -82.6730
> -0.0339   0.3843   0.9114  -121.5813
>  0.   0.   0. 1.
>
> In that transform the last column indicates the image's origin. However, I 
> was unable to find the relation between the information available in the 
> DICOM header and this transform.
>
> Best,
> Falk
>
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Greve, Douglas 
> N.,Ph.D.
> Gesendet: Donnerstag, 2. Mai 2019 17:33
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] Primary slice direction and image origin?
>
> You can use --slicedirection to get the slice direction (it will also get 
> printed out by just running mri_info on a file). What do you mean by the 
> image origin?
>
> On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>>  External Email - Use Caution
>>
>> Dear all,
>>
>> This is not directly related to FreeSurfer, however, can anyone tell 
>> me how the primary slice direction and image origin is determined 
>> from the DICOM header as displayed for example using mri_info?
>>
>> Best,
>>
>> Falk
>>
>> ...
>>
>> klinikum_logo_schmal_e-mail_blau
>>
>> *Universitätsklinik für Neurologie*
>>
>>
>> Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät 
>> Leipziger Str. 44
>> 39120 Magdeburg
>>
>> *Telefon: *+49-391-6117-512
>>
>> *falk.luesebr...@med.ovgu.de *
>> *http://www.kneu.ovgu.de/kneu.html*
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Longitudinal processing

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear all,

I'm a beginner in using the longitudinal processing pipeline (as well as 
statistical analysis) and it would be great to get some insights or hints to 
analyze my data.

I have a dataset consisting of 11 subjects each acquired at 7 different time 
points with an isotropic resolution of 1 and 0.8 mm at 3T using a 64-channel 
head coil. Using that dataset I want to investigate short term differences in 
e.g. cortical thickness with the goal to assess the degree of biological 
variance during that time period.

I have plotted the mean cortical thickness of each time point of every subject 
(using lme_timePlot and lme_lowessPlot) showing a somewhat random distribution 
across time and from my perspective fairly high standard deviation. I wanted to 
have a look at the individual percent change by overlaying the symmetric 
percent change on fsaverage, but wasn't quite sure of the scale. Is it in 
percent? So in case I set the scale bar between 1 and 5, the color relates to 1 
to 5 percent?

What other ways would make sense to have a look at? I definitely cannot compare 
groups, as there is just one. The days and time of acquistion are rather 
randomly choosen, so I potentially cannot use either as a covariate.

Best,
Falk

...

[klinikum_logo_schmal_e-mail_blau]
University Clinic for Neurology

Otto-von-Guericke-university Magdeburg
Medical faculty
Leipziger Str. 44
39120 Magdeburg

Phone +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Postdotoral call, human brain microstructure with MRI, Italy

[Jovicich, Jorge]

External Email - Use Caution

A 2-year postdoctoral call is available at the MRI Group of the Center 
for Mind/Brain Sciences  (CIMeC) at the University of Trento, Italy. The 
focus of this position will involve the development, testing and 
validation of MRI techniques that allow quantification of function and 
tissue microstructure properties.

The successful candidate will be part of an international 
multidisciplinary team developing and applying MRI techniques to study 
brain structure and function supporting normal higher cognitive function 
as well as the study of cognitive dysfunction in various neurological 
and neuropsychiatric conditions (including pre-surgical planning, 
plasticity in deaf and blind, novel markers sensitive
to the progression of neurodegenerative diseases).

Facilities: The CIMeC MRI neuroimaging lab uses a Siemens Prisma 3T 
scanner designed for research and clinical studies. The position will 
allow for training opportunities in pulse sequence development, brain 
anatomy, and translational clinical research.
The fellow is expected to be able to work independently as well as part 
of a multidisciplinary team with supervisory responsibilities of 
graduate student research. The fellow will support research MRI users, 
will have opportunities to develop new ideas and advance their own 
research interests in an international academic environment. Beyond 
work, there are outstanding opportunities for enjoying outdoors activities.

Requirements: Minimum qualifications are a doctoral degree in cognitive 
neurosciences, physics, engineering, computer sciences or related area, 
strong scientific publication record, and demonstrated expertise in MRI 
methods development and applications. The ideal candidates should be 
proficient in programming, such as C++, Matlab. Experience in pulse 
sequence design, particularly on Siemens platform, and/or image 
reconstruction will be a plus. Additional requirements include high 
self-motivation, ability of solving research problems independently, and 
excellent communication skills.

Contact:  Jorge Jovicich, Ph.D, MSc, Associate Professor 
(jorge.jovic...@unitn.it)
      Attending ISMRM, contact me for an informal meeting if 
interested

Postdoc call: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer